Setup

Configuring your system for the project.

Conda Environment

Preparing the local environment.

1. conda create -n tox python=3.9

2. conda activate tox

3. conda install -c conda-forge biopython

4. conda install -c pytorch pytorch

5. conda install scikit-learn

Jupyter Notebook

Making Conda available in Jupyter.

1. conda install -c anaconda ipykernel

2. python -m ipykernel install --user --name=tox

Files

    Contains data from previous papers,
    including ToxIBTL, ToxDL & ToxinPred.

    Contains Python files for exploratory data analysis.

    This includes the reading in and wrangling of data into
    a standard format ( sequences and toxic / non-toxic ),
    identification of duplicate sequences, division of data
    into training and test, as well as analysis of sequence
    similarity.

    Contains data related to CD-HIT, which we use to
    determine sequences that are at least 40% similar.

    Contains Jupyter notebooks used in the
    process of developing our ToxIN model.

    The /ToxIBTL/ folder contains
    original code from ToxIBTL.